What's new in CodonCode Aligner 3.0

See all amino acid translations

Simply switch between showing bases and amino acid
translations for each of your samples. Choose between translation-based
background colors, colored nucleotides, or quality-based background
colors. Independent from the background, select to see the bases or the
amino acid translation for your sequences. Quickly change the reading
frame by toolbar button or menu. See and print translations in contigs,
with chromatograms, or when looking at base views.

Spot the differences

Easily spot the differences in your contigs by
looking at the new Difference Table. Navigate to these differences
simply by clicking on any cell in the difference table. Use different
filters to control what to display in your Difference Tables. Switch
between compact size for overviews and a larger size for details.
Export the results.

Import from GenBank

Automate with scripts

Use scripts to facilitate your daily work. Many
new script commands make scripting in CodonCode Aligner better than
ever. Choose to run a script when starting CodonCode Aligner or
access your scripts quickly through the new script menu.

Create new text sequences

Easily create new text sequences using copy and
paste. CodonCode Aligner automatically parses known formats like
Genbank or FASTA from the clipboard to create single or mutiple new
sequences.

Do more, faster

Reduced memory use allows you to work with 3 x
larger projects. Assembly and alignment has been optimized to be
substantially faster when working with thousands of samples. Import 454
data from SFF files, and assemble by multiplex ID tags.

Example of substantially faster
assemblies on a test data set. Speed improvements increase with project
size and depth of coverage.

More...

Improved handling for pen tablets

More control when exporting in FASTA format:
Control the replacement of spaces or other
problematic characters in
sequence names. Append the number of sequences in contigs to the file.
Append comments. Add gaps at the start and end of sequences in contigs,
to allow import of aligned contigs in other programs.

Automatic memory handling on Windows: CodonCode
Aligner will now automatically use as
much memory
as is needed and available (up to 1.4 GB), without the need to edit
.ini files.

Monitor memory use in the project
view: Wondering if you can add more sequences to you
project? You can now monitor
how much memory CodonCode Aligner uses directly in the project view.

Remove leading and trailing contig gaps at
import: Gaps
are removed automatically from the start and end of sequences when
importing contigs from FASTA (and similar) files.

Contigs sorted by size: After
assemblies, contigs are now sorted by the number of samples they
contain before naming.

Improved end clipping: End
clipping for sequences that contain many Ns (with unreasonably high
quality scores due to a KB basecalller bug) now works better.

The new features and improvements listed above describe
what is new in CodonCode Aligner version 3.0. The CodonCode Aligner version history shows a comparison of the features available in different versions. New features introduced
in previous Aligner releases are described separately for CodonCode
Aligner 2.0, 1.6, 1.5, and 1.4.